Human Cell Atlas

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Human Cell Atlas
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DescriptionThe Human Cell Atlas is a global consortium that is creating detailed maps of the cells in the human body to transform understanding of health and disease.
Organisms Human
Contact
Primary citationRegev, Aviv; et al. (Human Cell Atlas Organizing Committee) (2018). "The Human Cell Atlas White Paper". arXiv: 1810.05192 [q-bio.TO].
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Website www.humancellatlas.org

The Human Cell Atlas is a global project to describe all cell types in the human body. [1] The initiative was announced by a consortium after its inaugural meeting in London in October 2016, which established the first phase of the project. [2] [3] Aviv Regev and Sarah Teichmann defined the goals of the project at that meeting, [4] which was convened by the Broad Institute, the Wellcome Trust Sanger Institute and Wellcome Trust. [5] Regev and Teichmann lead the project. [6] As of 2024, the project has mapped approximately 62 million human cells into 18 biological networks, which includes cells from vital systems such as the nervous system, lungs, heart, intestine and immune system. [7]

Contents

Description

The Human Cell Atlas will catalogue a cell based on several criteria, specifically the cell type, its state, its location in the body, the transitions it undergoes, and its lineage. [8] It will gather data from existing research, and integrate it with data collected in future research projects. [3] Among the data it will collect is the fluxome, genome, metabolome, proteome, and transcriptome. [3]

Its scope is to categorize the 37 trillion cells of the human body to determine which genes each cell expresses by sampling cells from all parts of the body. [9]

All aspects of the project will be made "available to the public for free", including software and results. [10]

By April 2018, the project included more than 480 researchers conducting 185 projects. [11]

Funding

In October 2017, the Chan Zuckerberg Initiative announced funding for 38 projects related to the Human Cell Atlas. [12] Among them was a grant of undisclosed value to the Zuckerman Institute of the Columbia University Medical Center at Columbia University. [10] The grant, titled "A strategy for mapping the human spinal cord with single cell resolution", will fund research to identify and catalogue gene activity in all spinal cord cells. [10] The Translational Genomics Research Institute received a grant to develop a standard for the "processing and storage of solid tissues for single-cell RNA sequencing", compared to the typical practice of relying on the average of sequencing multiple cells. [12] Project home pages are available at the Chan Zuckerberg Initiative's website. [13]

The program is also backed by European Union, the National Institutes of Health in the United States, and the Manton Foundation. [9]

Data

In April 2018, the first data set from the project was released, representing 530,000 immune system cells collected from bone marrow and cord blood. [11]

A research program at the Max Planck Institute of Immunobiology and Epigenetics published an atlas of the cells of the liver, using single-cell RNA sequencing on 10,000 normal cells obtained from nine donors. [14]

The Tabula Sapiens data was published on a dedicated website. [15]

See also

Notes

Related Research Articles

A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, that differ both in appearance and function yet have identical genomic sequences. Cells may have the same genotype, but belong to different cell types due to the differential regulation of the genes they contain. Classification of a specific cell type is often done through the use of microscopy. Recent developments in single cell RNA sequencing facilitated classification of cell types based on shared gene expression patterns. This has led to the discovery of many new cell types in e.g. mouse cortex, hippocampus, dorsal root ganglion and spinal cord.

<span class="mw-page-title-main">BGI Group</span> Chinese genome sequencing company

BGI Group, formerly Beijing Genomics Institute, is a Chinese genomics company with headquarters in Yantian, Shenzhen. The company was originally formed in 1999 as a genetics research center to participate in the Human Genome Project. It also sequences the genomes of other animals, plants and microorganisms.

<span class="mw-page-title-main">Max Planck Institute for Evolutionary Anthropology</span> Research institute based in Leipzig, Germany

The Max Planck Institute for Evolutionary Anthropology is a research institute based in Leipzig, Germany, that was founded in 1997. It is part of the Max Planck Society network.

<span class="mw-page-title-main">Wellcome Sanger Institute</span> British genomics research institute

The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.

<span class="mw-page-title-main">Human Genome Project</span> International scientific research project (1990–2003)

The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project began in 1984 by the US government, and it officially launched in 1990. It was declared complete on April 14, 2003, and included about 92% of the genome. Level "complete genome" was achieved in May 2021, with only 0.3% of the bases covered by potential issues. The final gapless assembly was finished in January 2022.

The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.

The Cancer Genome Project is part of the cancer, aging, and somatic mutation research based at the Wellcome Trust Sanger Institute in the United Kingdom. It aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States, the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis, treatment, and prevention through a better understanding of the molecular basis of the disease. The Cancer Genome Project was launched by Michael Stratton in 2000, and Peter Campbell is now the group leader of the project. The project works to combine knowledge of the human genome sequence with high throughput mutation detection techniques.

<span class="mw-page-title-main">David Haussler</span> American bioinformatician

David Haussler is an American bioinformatician known for his work leading the team that assembled the first human genome sequence in the race to complete the Human Genome Project and subsequently for comparative genome analysis that deepens understanding the molecular function and evolution of the genome.

The Cancer Genome Atlas (TCGA) is a project to catalogue the genomic alterations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of the disease.

Cancer genome sequencing is the whole genome sequencing of a single, homogeneous or heterogeneous group of cancer cells. It is a biochemical laboratory method for the characterization and identification of the DNA or RNA sequences of cancer cell(s).

<span class="mw-page-title-main">Aviv Regev</span> Bioinformatician

Aviv Regev is a computational biologist and systems biologist and Executive Vice President and Head of Genentech Research and Early Development in Genentech/Roche. She is a core member at the Broad Institute of MIT and Harvard and professor at the Department of Biology of the Massachusetts Institute of Technology. Regev is a pioneer of single cell genomics and of computational and systems biology of gene regulatory circuits. She founded and leads the Human Cell Atlas project, together with Sarah Teichmann.

<span class="mw-page-title-main">Dana Pe'er</span> Bioinformatician

Dana Pe'er, Chair and Professor in Computational and Systems Biology Program at Sloan Kettering Institute is a researcher in computational systems biology. A Howard Hughes Medical Institute (HHMI) Investigator since 2021, she was previously a professor at Columbia Department of Biological Sciences. Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer.

<span class="mw-page-title-main">Sarah Teichmann</span> German bioinformatician

Sarah Amalia Teichmann is a German scientist, the former head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, Professor at the University of Cambridge and Cambridge Stem Cell Institute, and is a senior research fellow at Churchill College, Cambridge.

<span class="mw-page-title-main">Chan Zuckerberg Initiative</span> American Philanthropic organization

The Chan Zuckerberg Initiative (CZI) is an organization established and owned by Facebook founder Mark Zuckerberg and his wife Priscilla Chan with an investment of 99 percent of the couple's wealth from their Facebook shares over their lifetime. The CZI is legally set up as a limited liability company (LLC) that can be seen as a for-profit charity and is an example of philanthrocapitalism. CZI has been deemed likely to be "one of the most well-funded Philanthropies in human history". Chan and Zuckerberg announced its creation on 1 December 2015, to coincide with the birth of their first child. Priscilla Chan has said that her background as a child of immigrant refugees and experience as a teacher and pediatrician for vulnerable children influences how she approaches the philanthropy's work in science, education, immigration reform, housing, criminal justice, and other local issues.

The Earth BioGenome Project (EBP) is an initiative that aims to sequence and catalog the genomes of all of Earth's currently described eukaryotic species over a period of ten years. The initiative would produce an open DNA database of biological information that provides a platform for scientific research and supports environmental and conservation initiatives. A scientific paper presenting the vision for the project was published in PNAS in April 2018, and the project officially launched November 1, 2018.

<span class="mw-page-title-main">Muzlifah Haniffa</span> Malaysian dermatologist and immunologist

Muzlifah Haniffa is a Malaysian dermatologist and immunologist who focuses on the development of the immune system and the use of single-cell techniques to understand biology. Haniffa is a professor and Wellcome Trust Senior Research Fellow in the Faculty of Medical Sciences at Newcastle University.

Barbara Elizabeth Engelhardt is an American computer scientist and specialist in bioinformatics. Working as a Professor at Stanford University, her work has focused on latent variable models, exploratory data analysis for genomic data, and QTLs. In 2021, she was awarded the Overton Prize by the International Society for Computational Biology.

The Cell Ontology is an ontology that aims at capturing the diversity of cell types in animals. It is part of the Open Biomedical and Biological Ontologies (OBO) Foundry. The Cell Ontology identifiers and organizational structure are used to annotate data at the level of cell types, for example in single-cell RNA-seq studies. It is one important resource in the construction of the Human Cell Atlas.

John Marioni is a Senior Vice President and Head of Computation at Genentech Research and Early Development (gRED) in South San Francisco. Previously he was the Head of Research at the European Bioinformatics Institute and held an appointment at the Wellcome Sanger Institute and the Cancer Research UK Cambridge Institute in Cambridge University. He is a computational biologist known for his research on statistical and computational methods for the analysis of genomics data, in particular single-cell biology and evolutionary genomics. He continues to co-chair the Human Cell Atlas Analysis Working Group.

References

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